Molecular mechanisms of transgenerational epigenetic inheritance

Nature Reviews Genetics, Год журнала: 2022, Номер 23(6), С. 325 - 341

Опубликована: Янв. 4, 2022

Язык: Английский

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3D genomics across the tree of life reveals condensin II as a determinant of architecture type

Science, Год журнала: 2021, Номер 372(6545), С. 984 - 989

Опубликована: Май 27, 2021

We investigated genome folding across the eukaryotic tree of life. find two types three-dimensional (3D) architectures at chromosome scale. Each type appears and disappears repeatedly during evolution. The architecture that an organism exhibits correlates with absence condensin II subunits. Moreover, depletion converts human to a state resembling seen in organisms such as fungi or mosquitoes. In this state, centromeres cluster together nucleoli, heterochromatin domains merge. propose physical model which lengthwise compaction chromosomes by mitosis determines chromosome-scale architecture, effects are retained subsequent interphase. This mechanism likely has been conserved since last common ancestor all eukaryotes.

Язык: Английский

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Toward a genome sequence for every animal: Where are we now?

Proceedings of the National Academy of Sciences, Год журнала: 2021, Номер 118(52)

Опубликована: Дек. 3, 2021

In less than 25 y, the field of animal genome science has transformed from a discipline seeking its first glimpses into sequences across Tree Life to global enterprise with ambitions sequence genomes for all Earth’s eukaryotic diversity [H. A. Lewin et al. , Proc. Natl. Acad. Sci. U.S.A. 115, 4325–4333 (2018)]. As rapidly moves forward, it is important take stock progress that been made best inform discipline’s future. this Perspective, we provide contemporary, quantitative overview sequencing. We identified available assemblies in GenBank, world’s most extensive genetic database, 3,278 unique species 24 phyla. assessed taxonomic representation, assembly quality, and annotation status major clades. show while tremendous occurred, stark disparities genomic representation exist, highlighted by systemic overrepresentation vertebrates underrepresentation arthropods. terms long-read sequencing dramatically improved contiguity, whereas gene annotations are just 34.3% taxa. Furthermore, diversified recent years an ever-expanding pool researchers participating. However, still appears be dominated institutions Global North, which have listed as submitting institution 77% assemblies. conclude offering recommendations improving resource availability research value also broadening representation.

Язык: Английский

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Why sequence all eukaryotes?

Proceedings of the National Academy of Sciences, Год журнала: 2022, Номер 119(4)

Опубликована: Янв. 18, 2022

Life on Earth has evolved from initial simplicity to the astounding complexity we experience today. Bacteria and archaea have largely excelled in metabolic diversification, but eukaryotes additionally display abundant morphological innovation. How these innovations come about what constraints are there origins of novelty continuing maintenance biodiversity Earth? The history life code for working parts cells systems written genome. BioGenome Project proposed that genomes all extant, named eukaryotes—about 2 million species—should be sequenced high quality produce a digital library Earth, beginning with strategic phylogenetic, ecological, high-impact priorities. Here discuss why should sequence eukaryotic species, not just representative few scattered across many branches tree life. We suggest questions evolutionary ecological significance will only addressable when whole-genome data representing divergences at branchings or species natural ecosystems available. envisage genomic foster understanding ongoing processes speciation, adaptation, organismal dependencies within entire ecosystems. These explorations resolve long-standing problems phylogenetics, evolution, ecology, conservation, agriculture, bioindustry, medicine.

Язык: Английский

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Repeat-based holocentromeres influence genome architecture and karyotype evolution

Cell, Год журнала: 2022, Номер 185(17), С. 3153 - 3168.e18

Опубликована: Авг. 1, 2022

The centromere represents a single region in most eukaryotic chromosomes. However, several plant and animal lineages assemble holocentromeres along the entire chromosome length. Here, we compare genome organization evolution as function of type by assembling chromosome-scale holocentric genomes with repeat-based from three beak-sedge (Rhynchospora pubera, R. breviuscula, tenuis) their closest monocentric relative, Juncus effusus. We demonstrate that transition to holocentricity affected 3D architecture redefining genomic compartments, while distributing thousands units genome-wide. uncover complex pubera hides its unexpected octoploidy describe marked reduction number for tenuis, which has only two show fusions, facilitated holocentromeres, promoted karyotype diploidization. Our study thus sheds light on important aspects influenced organization.

Язык: Английский

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Three-dimensional genome rewiring in loci with human accelerated regions

Science, Год журнала: 2023, Номер 380(6643)

Опубликована: Апрель 27, 2023

Human accelerated regions (HARs) are conserved genomic loci that evolved at an rate in the human lineage and may underlie human-specific traits. We generated HARs chimpanzee with automated pipeline alignment of 241 mammalian genomes. Combining deep learning chromatin capture experiments neural progenitor cells, we discovered a significant enrichment topologically associating domains containing variants change three-dimensional (3D) genome organization. Differential gene expression between humans chimpanzees these suggests rewiring regulatory interactions neurodevelopmental genes. Thus, comparative genomics together models 3D folding revealed enhancer hijacking as explanation for rapid evolution HARs.

Язык: Английский

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Genome control by SMC complexes

Nature Reviews Molecular Cell Biology, Год журнала: 2023, Номер 24(9), С. 633 - 650

Опубликована: Май 25, 2023

Язык: Английский

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The ENCODE Uniform Analysis Pipelines

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Апрель 6, 2023

Abstract The Encyclopedia of DNA elements (ENCODE) project is a collaborative effort to create comprehensive catalog functional in the human genome. current database comprises more than 19000 genomics experiments across 1000 cell lines and tissues using wide array experimental techniques study chromatin structure, regulatory transcriptional landscape Homo sapiens Mus musculus genomes. All data, metadata, associated computational analyses created by ENCODE consortium are submitted Data Coordination Center (DCC) for validation, tracking, storage, distribution community resources scientific community. has engineered distributed uniform processing pipelines order promote data provenance reproducibility as well allow interoperability between genomic other consortia. files, reference genome versions, software parameters used captured available via Portal. pipeline code, developed Docker Workflow Description Language (WDL; https://openwdl.org/ ) publicly GitHub, with images on Dockerhub ( https://hub.docker.com ), enabling access diverse range biomedical researchers. maintained DCC can be installed run personal computers, local HPC clusters, or cloud computing environments Cromwell. Access allows small labs ability use without institutional compute clusters. Standardization methodologies analysis quality control leads comparable results from different collections - prerequisite successful integrative analyses. Database URL: https://www.encodeproject.org/

Язык: Английский

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The little skate genome and the evolutionary emergence of wing-like fins

Nature, Год журнала: 2023, Номер 616(7957), С. 495 - 503

Опубликована: Апрель 12, 2023

Skates are cartilaginous fish whose body plan features enlarged wing-like pectoral fins, enabling them to thrive in benthic environments1,2. However, the molecular underpinnings of this unique trait remain unclear. Here we investigate origin phenotypic innovation by developing little skate Leucoraja erinacea as a genomically enabled model. Analysis high-quality chromosome-scale genome sequence for shows that it preserves many ancestral jawed vertebrate compared with other sequenced genomes, including numerous ancient microchromosomes. Combining comparisons extensive regulatory datasets fins-including gene expression, chromatin occupancy and three-dimensional conformation-we find skate-specific genomic rearrangements alter landscape genes involved planar cell polarity pathway. Functional inhibition signalling resulted reduction anterior fin size, confirming pathway is major contributor batoid morphology. We also identified fin-specific enhancer interacts several hoxa genes, consistent redeployment hox expression confirmed its potential activate transcription using zebrafish reporter assays. Our findings underscore central role reorganization variation evolution phenotypes, shedding light on an enigmatic trait.

Язык: Английский

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Rules of engagement for condensins and cohesins guide mitotic chromosome formation

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Апрель 18, 2024

Abstract During mitosis, interphase chromatin is rapidly converted into rod-shaped mitotic chromosomes. Using Hi-C, imaging, proteomics and polymer modeling, we determine how the activity interplay between loop-extruding SMC motors accomplishes this dramatic transition. Our work reveals rules of engagement for complexes that are critical allowing cells to refold We find condensin disassembles loop organization by evicting or displacing extrusive cohesin. In contrast, bypasses cohesive cohesins, thereby maintaining sister chromatid cohesion while separating sisters. Studies chromosomes formed cohesin, II I alone in combination allow us develop new models chromosome conformation. these models, loops consecutive not overlapping, implying condensins do freely pass one another but stall upon encountering each other. The dynamics Hi-C interactions morphology reveal during prophase extruded vivo at ∼1-3 kb/sec as they form a disordered discontinuous helical scaffold within individual chromatids.

Язык: Английский

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